The Chemical Basis of Life

Atoms, Molecules, and Water-

All life forms are composed of matter, the smallest part of matter being atoms.

Atoms- Anything that contains mass and occupies space

  • Matter exists in 3 different states: Solid, Liquid, and Gas

  • Atoms cannot be further broken down into other substances by ordinary chemical or physical means.

Atoms are composed of 3 Subatomic Particles in a Nucleus-

  • Protons (p+)

  • Neutrons(N0)

  • Electrons(e-)

The Nucleus consists of protons and neutrons, and electrons are on the outside of the nucleus.

In most atoms, the number of protons and electrons is identical, but the number of neutrons may vary.

The entire atom does not have any charge, because the number of electrons and the number of protons cancel each other out.

What is a chemical element?- Each specific type of atom, such as nitrogen, hydrogen, oxygen, and so on, is called an element.

Orbital- the region where an electron is most likely found.

  • An orbital can contain a maximum of two electrons.

Each atom has several electron shells or energy levels. The electron shells are numbered, with shell 1 being closest to the nucleus. The orbitals and the electron shells work simultaneously.

Each chemical element has a unique number of protons

  • The number of protons in an atom is its atomic number

  • Ex. Hydrogen contains 1 proton. Its atomic number is 1. Its atomic mass is 1.008

Periodic table-The periodic table is organized in each row, where each row indicates the number of electron shells.

  • Each element is located in a specific cell (place) according to the number of its electrons (atomic number)

Chemical Bonds and Molecules

Molecule- Two or more atoms bonded together to make up a molecule

Example- Water(H2O) has two hydrogen atoms and one oxygen atom bonded together.

When atoms convert to molecules by bonding to other atoms, their properties change completely.

Covalent Bonds- formed when atoms share electrons

Different types of covalent bonds-

Single bond- two atoms share a air of electron

Double bond- two atoms share two pairs of electrons

Triple bond- two atoms share two pairs of electrons

The electronegativity of an atom- The ability of an atom to attract electrons in a bond with another atom

  • Electronegativity is the tendency to attract the shared pair of electrons. These are polar covalent bonds

  • Ex. water molecule (2 hydrogen, 1 oxygen). Oxygen is much more electronegative than hydrogen; the shared electrons tend to be pulled closer to the oxygen

Hydrogen Bond

  • Forms when a hydrogen atom, already covalently bonded to a high electronegative atom (like nitrogen, oxygen, or fluorine) is attracted to another electronegative atom in a different molecule.

  • Relatively weak compared to covalent bonds but still play a crucial role in many biological and chemical processes.

Formation of hydrogen bonds in water

  • Oxygen is more electronegative than hydrogen, which means it attracts electrons more strongly

    As a result, the electrons in the covalent bonds between hydrogen and oxygen are pulled closer to the oxygen atom.

    The oxygen atom in a water molecule develops a partial negative charge (δ-) because it has more electrons around it.

    The hydrogen atoms, having lost some of their electron density to oxygen, carry partial positive charges (δ+).

    Hydrogen bonds in water form between the partially positively charged hydrogen atom (δ+) of one water molecule and the partially negatively charged oxygen atom (δ-) of another water molecule.

Nonpolar Bond

Polar Bond

  • When two atoms wit different electronegativities form a covalent bond

  • The shared electrons are more likely to be closer to the nucleus of the atom of the higher electronegativity than the atom of lower electronegaivity

Ionic Bond

  • Involve an attraction between positive and negative ions

  • atoms are electrically neutral because they

Difference between ionic and covalent bonds: Covalent bonds share electrons while ionic bonds transfer electrons.

Electronegativity is the ability of an atom to attract electrons in a bond

All living organisms are made up of biomolecules

Biomolecules are essential organic molecules that support the maintenance and metabolism of living organisms

Examples:

  • Lipids

  • Nucleic acid

  • Carbohydrates

  • Proteins

Large biomolecules are called macromolecules (the ones above)

Small biomolecules are called organic molecules

Functional groups- part of all biomolecules that have specific behaviors

  1. Hydroxyl Group (-OH):

  • present in alchohols and carbohydrates

  • It impairs properties like solubility in water and the ability to form hydrogen bonds

  1. Carbonyl Group (C=O)

  • Are functional groups of carbohydrates, lipids, and proteins

  • Essential in chemical reactions, such as condensation and hydrolysis

  1. Carbonxl Group

  • Can act as acids by donating protons

  1. Amino Group (-NH2)

  • found in amino acids

  • It can act as a base by accepting protons, unlike carbonyl group

  1. Phosphates group (-PO4)

  • Phosphate groups are crucial in the structure of nucleic acids (DNA and RNA)

  1. Sulfhydryl Group (-SH)

  • This group plays a role in stabilizing protein structures through the formation of disulfide bonds

  1. Methyl Group (-CH3)

  • found in various biomolecules, including DNA and some lipids

  • Can play a role in gene expression regulation

  1. Ester group(-COO-)

  • Present in lipids

  • Involved in energy storage and cell membrane structure

  1. Amid group (-CONH2)

  • found in proteins

  • Link amino acids together in peptide bonds

  • Present in nucleic acids